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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
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How to Deal Metallo-proteins with an Organic Molecule as a Ligand? #34

Closed Ash1000 closed 1 year ago

Ash1000 commented 1 year ago

Hello, I came to know that GAFF failed to parameterize the metal ions, as a result, the organic molecule (ligand) jumped out of the pocket. On closer inspection of the test run, where I tried both GAFF and OpenFF, both have removed the metal ions (Zn in my case). Would please guide, if there is any other way of handling it, using these notebooks?

pablo-arantes commented 1 year ago

Hi @Ash1000,

Sorry for my delay. Unfortunately, our notebook does not accept metal ions. We need to change the code to accept this type of proteins. We are working on that, I will let you know when it's ready.

Thank you.

Best,

Pablo.

P.S: I will close the other issue regarding the volume, I suppose the issue was the ligand PDB. Right?